1. Field
The claimed subject matter relates to structured documents containing three dimensional and two dimensional objects along with their related information, and methods, systems and computer programs for authoring and viewing the structured documents.
2. Related Art
A number of different types of molecular modeling programs are known and used to produce and represent three dimensional molecular structures on at least one computing platform. This prior art typically makes use of one or more databases in order to organize the three dimensional information and in use, the one or more databases are accessed separately. The data from the one or more databases is then combined into a single screen output to the user, often creating problems with displaying diverse amounts of information.
The prior art includes various methods for disseminating and browsing annotated 3D molecular information. For instance, PDB file format viewers read PDB formatted files which are distributed by the Protein Data Bank (PDB.) The RasMol program, found on the internet at http://www.umass.edu/microbio/rasmol/ is one example of a PDB viewer. Other file formats such as CN3D, have their own viewers such as the CN3D viewer found on the internet at:
http://www.biosino.org/mirror/www.ncbi.nlm.nih.gov/Structure/cn3d/. Other general molecular viewing and graphics computer programs include Insight by Accelrys, Sybyl by Tripos, MOE by Chemical Computing Group and some previously published versions of the ICM-Browser by Molsoft including those versions below version 2.3.
Other non-molecular based viewers found in the prior art which allow a user to view or present data include the Powerpoint and Word programs by Microsoft and the Acrobat Program and Reader by Adobe Corporation. These viewers cannot read or display known molecular file formats and they are unable to display interactive molecular animations or transitions.
For instance, the Adobe Acrobat PDF file format used by the Adobe Acrobat reader displays one dimensional images of molecular representations which are typically displayed in the form of an embedded picture. Additional molecular graphics software is also required to generate these images. This is also the case for many internet web pages known in the art which require the use of more than one file which are located in directories of images and HTML documents.
Other viewers and browsers known in the prior art include internet (web) and Java based browsers and HTML-browser dependent plug-ins such as JMOL located on the internet at http://jmol.sourceforge.net/, and animation browsers such as the Kinemage files browser located on the internet at http://kinemage.biochem.duke.edu/ and MD trajectory viewers.
Further, these prior art viewers and prior art molecular file formats require a number of command triggers (such as mouse clicks and store commands) for a user of the viewer to accomplish basic tasks such as the creation of new files. For example, the applications Kinemage, JMOL and WebMol require a user to continually click and hold down a mouse button in order to rotate a molecule in the X, Y or Z directions or in order to view multiple images leading to an animated effect. Additionally, many of these viewers have predefined or default molecule rotations which are not able to be altered or manipulated.
Molecular animations include molecular or three dimensional transitions from one position in three dimensional space to another position. The above referenced prior art viewers employ various methods for molecular animations which are burdensome and which involve multiple steps which are required to be taken by the user.
Using these viewers, many individual animations are usually required to highlight a single idea and each animation needs to be pasted into the application. Once the animation is embedded in the viewer, it is fixed and changes are difficult to make without creating a new file. For example, in Microsoft PowerPoint it is necessary to create an animation using an additional piece of software. Once created, the animation is imported into the PowerPoint application. This is usually a time consuming process requiring knowledge of many different software applications and file types. The resulting animation file is generally large with additional files needed to be merged into a single file, and that file typically needs to be packaged and unpackaged in archive file format due to the large sizes of the embedded objects.
Prior art publications include U.S. Publication No. 2004/0170949 to O'Donoghue, et al. which describes a method and apparatus for depicting one or more biological elements in a basic environment by means of a data processing system comprising the steps of obtaining one or more data sets relating to a biological element, determining at least one first feature element from said data sets, said feature element providing information on a relation between said biological element and said basic environment, obtaining data determining a graphical representation for depicting at least one of the biological elements corresponding to said one or more data sets determining a relation between the graphical representation of said basic environment and said graphical representation on the basis of said first feature element, providing means for effecting that in a graphical representation of said environment generated from said data said graphical representation of said biological element is depicted as located on said display of said basic environment element according to said relation determined on the basis of said first feature element. This invention also provides for a method and apparatus for handling three-dimensional representations of biological molecules, such as proteins and protein complexes.
While prior art includes various methods and apparatuses for representing three dimensional objects, none are able to view those structures address using a single file, single-browser, platform independent method and viewer to view a document or a multi-slide presentation containing different animated and interactive molecular views in the environment of text, sequence, alignments and other data and without explicit representation of animation frames or coordinates.